Methods and compositions of targeted drug development

Abstract

Provided herein are compounds having anti-proliferative effect. Also provided are compounds that can modulate the activity of multi-domain proteins comprising a dimerization arm and interdomain tether, such as EGFR, where an untethered, extended conformation is the active state and a tethered conformation is the inactive state, resulting in an autoinhibited configuration. Also provided are methods and pharmacophores for identifying such compounds. Other aspects provide methods or therapeutic treatment for proliferative diseases, disorders, or conditions, such as those associated with EGFR.

What is claimed is: 
     
       1. A compound having a formula of: 
       
         
           
           
               
               
           
         
         or a stereoisomer or pharmaceutically acceptable salt thereof; 
         wherein,
 X is selected from the group consisting of: hydrogen, 2-Methyl, 5-Chloro, 5-Nitro, and 6-Hydroxyl; 
 R 1  is selected from the group consisting of:
 (i) a 2-Pyridyl ring of Formula (3) 
 
 
       
       
         
           
           
               
               
           
         
         
           
             
               wherein 
                R 23  is selected from the group consisting of hydrogen; fluoro; chloro; trifluoromethyl; methyl; ethyl; and methoxy; 
                R 3  is selected from the group consisting of hydrogen; fluoro; chloro; methyl; ethyl; methoxy; a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; and alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 
                R 24  is selected from the group consisting of: hydrogen; fluoro; chloro; and trifluoromethyl; and 
                R 4  is selected from the group consisting of hydrogen; methyl; a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; and alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 
             
             (ii) a 3-Pyridyl ring of Formula (4) 
           
         
       
       
         
           
           
               
               
           
         
         
           
             
               wherein R 5 , R 6 , and R 7  are independently selected from the group consisting of: hydrogen, a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; Aryl comprising a phenyl or heteroaryl containing from 1 to 4 N, O, or S atoms; and alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; and 
             
             (iii) a 4-Pyridyl ring of Formula (5) 
           
         
       
       
         
           
           
               
               
           
         
         
           
             
               wherein R 8  and R 9  are independently selected from the group consisting of: a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl containing from 1 to 4 N, O, or S atoms; and alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; and 
             
           
           R 2  is selected from the group consisting of:
 (i) an unsubstituted phenyl ring or a phenyl ring substituted at the 2-, 3-, 4-, 5- or 6-position with one or more groups independently selected from the group consisting of: straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 2,3-methylenedioxy; 3,4-methylenedioxy; dialkylamino having formula —NR 13 R 14  wherein R 13  and R 14  are independently selected from hydrogen or a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; trifluoromethyl; trifluoromethoxy; difluoromethoxy; 3,4-methylenedioxy; 2,3-methylenedioxy; nitro; and halogen;
 wherein if R 1  is a 3-Pyridyl ring of Formula (4) where each of R 5 , R 6 , and R 7  are hydrogen, and R 2  is a phenyl ring, the phenyl ring is substituted with one or more groups independently selected from the group consisting of: a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; a heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; alkoxy —OR 10  where R 10  is a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 2,3-methylenedioxy; 3,4-methylenedioxy; dialkylamino having formula —NR 13 R 14  wherein R 13  and R 14  are independently selected from hydrogen or a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; trifluoromethoxy; difluoromethoxy; 3,4-methylenedioxy; 2,3-methylenedioxy; and nitro; 
 
 (ii) a 2-Pyridyl ring substituted at 4- or 6-position of the pyridine ring with one or more groups independently selected from the group consisting of: straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation and C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 
 (iii) an unsubstituted 3-Pyridyl ring or a 3-Pyridyl ring substituted at the 2-, 4- or 6-position of the pyridine ring with one or more groups independently selected from the group consisting of: straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation and C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; and 
 (iv) an unsubstituted 4-Pyridyl ring or a 4-Pyridyl ring substituted at the 2- or 6-position of the pyridine ring with one or more groups independently selected from the group consisting of: straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation and C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 
 wherein if each of R 3 , R 4 , R 23 , and R 24  is hydrogen, then R 2  is a substituted pyridyl ring or a phenyl substituted with straight chain or branched C-3 to C-4 lower alkyl optionally containing unsaturation; C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; alkoxy —OR 10  where R 10  is a straight chain or branched C-3 to C-4 lower alkyl optionally containing unsaturation or a C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; 2,3-methylenedioxy; 3,4-methylenedioxy; dialkylamino having formula —NR 13 R 14  wherein R 13  and R 14  are independently selected from hydrogen or a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; trifluoromethoxy; difluoromethoxy; 3,4-methylenedioxy; 2,3-methylenedioxy; or nitro; 
 wherein if one of R 3 , R 4 , R 23 , or R 24  is methyl and the other three of R 3 , R 4 , R 23 , or R 24  are hydrogen, then R 2  is a substituted pyridyl ring or a phenyl substituted with straight chain or branched C-3 to C-4 lower alkyl optionally containing unsaturation; C-2 to C-6 cycloalkyl optionally containing unsaturation or one oxygen or nitrogen atom; aryl comprising a phenyl or heteroaryl five or six membered ring containing from 1 to 4 N, O, or S atoms; 2,3-methylenedioxy; 3,4-methylenedioxy; dialkylamino having formula —NR 13 R 14  wherein R 13  and R 14  are independently selected from hydrogen or a straight chain or branched C-1 to C-4 lower alkyl optionally containing unsaturation; trifluoromethyl; trifluoromethoxy; difluoromethoxy; 3,4-methylenedioxy; or 2,3-methylenedioxy; or 
 
         
         a stereoisomer or pharmaceutically acceptable salt thereof; and 
         Formula (2) excludes the compound of Formula (1): 
       
       
         
           
           
               
               
           
         
       
     
     
       2. The compound of  claim 1  wherein R 1  is a 2-pyridyl ring of Formula (3) and:
 R 24  is chloro; or 
 R 23  is methyl. 
 
     
     
       3. The compound of  claim 1  wherein R 1  is a 2-pyridyl ring of Formula (3) and:
 R 4  is hydrogen, R 24  is fluoro, R 3  is hydrogen, and R 23  is fluoro; 
 R 4  is methyl, R 24  is chloro, R 3  is hydrogen, and R 23  is fluoro; 
 R 4  is hydrogen, R 24  is chloro, R 3  is ethyl, and R 23  is fluoro; 
 R 4  is hydrogen, R 24  is fluoro, R 3  is methyl, and R 23  is fluoro; 
 R 4  is hydrogen, R 24  is chloro, R 3  is hydrogen, and R 23  is ethyl; 
 R 4  is methyl, R 24  is chloro, R 3  is hydrogen, and R 23  is chloro; 
 R 4  is hydrogen, R 24  is chloro, R 3  is methyl, and R 23  is fluoro; 
 R 4  is hydrogen, R 24  is trifluoromethyl, R 3  is hydrogen, and R 23  is hydrogen; 
 R 4  is hydrogen, R 24  is chloro, R 3  is hydrogen, and R 23  is methyl; 
 R 4  is hydrogen, R 24  is chloro, R 3  is hydrogen, and R 23  is chloro; 
 R 4  is hydrogen, R 24  is chloro, R 3  is methyl, and R 23  is hydrogen; or 
 R 4  is hydrogen, R 24  is chloro, R 3  is chloro, and R 23  is hydrogen. 
 
     
     
       4. The compound of  claim 1 , wherein R 1  is a 2-pyridyl ring of Formula (3) and:
 R 24  is chloro and R 3  is chloro or methyl or R 23  is chloro or methyl; 
 R 24  is chloro, R 3  is hydrogen, and R 23  is methyl; 
 R 24  is chloro, R 3  is methyl, and R 23  is fluoro; 
 R 24  is chloro, R 3  is chloro, and R 23  is hydrogen; 
 R 24  is chloro, R 3  is hydrogen, and R 23  is chloro. 
 
     
     
       5. The compound of  claim 1  wherein R 2  is selected from the group consisting of:
 a phenyl ring substituted at the 2- and 4-positions; 
 4-trifluoromethylphenyl; 
 2-fluoro,4-trifluoromethylphenyl; and 
 2,4-dichlorophenyl. 
 
     
     
       6. The compound of  claim 1  wherein R 2  is selected from the group consisting of: 4-chlorophenyl; 2-fluoro,4-trifluoromethylphenyl; 3-fluoro,4-chlorophenyl; 2-fluoro,4-chlorophenyl; 2,3-dichlorophenyl; 2,3,5-trichlorophenyl; 2,4-dichlorophenyl; 3,4-dichlorophenyl; and 3,5-dichlorophenyl. 
     
     
       7. The compound of  claim 1  wherein R 2  is selected from the group consisting:
 a phenyl ring substituted at the 4 position with chloro and substituted at the 2- or 3-position with chloro or fluoro; 
 2,4-dichlorophenyl; and 
 2-chloro,4-fluorophenyl. 
 
     
     
       8. The compound of  claim 1  wherein Formula (2) is not one or more of the following compounds: 
       
         
           
           
               
               
           
         
       
     
     
       9. The compound of  claim 1  that inhibits EGFR activity comprising:
 six or more of functional groups F(I)1, F(I)2, F(I)3, F(I)4, F(I)5, F(I)6, F(I)7, F(I)8, and F(I)9 of a Scheme 11505-like pharmacophore; 
 wherein
 functional group F(I)1 donates an H-bond or forms a salt bridge to a carboxylate side chain of receptor Asp553 of SEQ ID NO: 1 and has coordinates of r=56.363, θ (theta)=94.368, and φ (phi)=−17.752 and a spherical radius of about 1.2 {acute over (Å)}; 
 functional group F(I)2 donates an H-bond to backbone carbonyl of receptor Thr570 of SEQ ID NO: 1 and has coordinates of r=53.290, θ (theta)=101.494, and φ (phi)=−23.244 and a spherical radius of about 1.0 {acute over (Å)}; 
 functional group F(I)3 forms a hydrophobic contact with a side chain of receptor Val568, an imidazole side chain of receptor His566, and an imidazolidine ring of receptor Pro552 of SEQ ID NO: 1 and has coordinates of r=53.726, θ (theta)=97.830, and φ (phi)=−18.378 and a spherical radius of about 1.7 {acute over (Å)}; 
 functional group F(I)4 donates an H-bond or forms a salt bridge to the side chain carboxylate of receptor Asp563 of SEQ ID NO: 1 and has coordinates of r=56.103, θ (theta)=99.536, and φ (phi)=−21.080 and a spherical radius of about 1.2 {acute over (Å)}; 
 functional group F(I)5 forms a hydrophobic contact with an imidazoline ring of receptor Pro572 and a side chain of Met253 of SEQ ID NO: 1 and has coordinates of r=53.647, θ (theta)=103.844, and φ (phi)=−20.990 and a spherical radius of about 1.4 {acute over (Å)}; 
 functional group F(I)6 donates an H-bond to a backbone carbonyl of receptor Cys571 of SEQ ID NO: 1 and has coordinates of r=51.088, θ (theta)=104.241, and φ (phi)=−25.552 and a spherical radius of about 1.2 {acute over (Å)}; 
 functional group F(I)7 donates an H-bond to a backbone carbonyl of receptor Cys571 of SEQ ID NO: 1 and has coordinates of r=52.340, θ (theta)=103.980, and φ (phi)=−27.461 and a spherical radius of about 1.5 {acute over (Å)}; 
 functional group F(I)8 accepts an H-bond from receptor backbone NH of Ala573 of SEQ ID NO: 1 and has coordinates of r=51.383, θ (theta)=106.455, and φ (phi)=−24.319 and a spherical radius of about 1.2 {acute over (Å)}; 
 functional group F(I)9 accepts an H-bond from receptor backbone NH of Ala573 of SEQ ID NO: 1 and has coordinates of r=52.861, θ (theta)=107.692, and φ (phi)=−25.447 and a spherical radius of about 1.5 {acute over (Å)}; and 
 the compound substantially maintains a non-extended tether inactive configuration of EGFR or substantially prevents stabilization of an extended tether active configuration of EGFR. 
 
 
     
     
       10. A method for forming a compound of  claim 1 , comprising:
 combining an amino pyridine intermediate compound, an aldehyde intermediate compound, and a hydroxyquinoline intermediate compound in ethanol under conditions sufficient to form a compound of  claim 1 ; 
 wherein,
 the amino pyridine intermediate compound comprises R 2 —CHO, where R 2  is as defined in  claim 1 ; 
 the aldehyde intermediate compound comprises R 1 —NH 2 , where R 1  is as defined in  claim 1 ; and 
 the hydroxyquinoline intermediate compound comprises 8-hydroxyquinoline, optionally substituted with X, where X is as defined in  claim 1 . 
 
 
     
     
       11. The method of  claim 10 , wherein the aminopyridine intermediate compound is selected from the group consisting of 2-Amino-3-methoxy-5-chloropyridine; 2-Amino-4,5-dichloropyridine; 2-Amino-5-chloro-6-methylpyridine; 2-Amino-5-chloro-3-methylpyridine; 2-Amino-3,5-dichloro-4-methylpyridine; 2-Amino-3,5-dichloro-4,6-dimethylpyridine; 2-Amino-3-fluoro-4-methyl-5-chloropyridine; 2-Amino-3-ethyl-5-chloropyridine; 2-Amino-3-fluoro-4-ethyl-5-chloropyridine; and 2-Amino-4-methyl-3,5-difluoropyridine, or an aminopyridine compound formed according to  claim 18 . 
     
     
       12. The method of  claim 10 , wherein the aminopyridine intermediate compound is formed by a method comprising:
 (i) combining a substituted or unsubstituted 2-aminopyridine and N-chlorosuccinimide in a solvent comprising ethylacetate or dimethylformamide under conditions sufficient to form a 2-amino-5-chloropyridine derivative; or 
 (ii) combining acetic anhydride in glacial acetic acid and a 2-aminopyridine substituted at 3-position and 5-position with fluoro, chloro, or bromo to form a corresponding acetamide derivative; combining the acetamide derivative and diisopropyl amine and butyllithium in tetrahydrofuran at about −70° C. to deprotonate the acetamide derivative; combining the deprotonated acetamide derivative and a lower alkyl halide to alkylate the 4-position of the acetamide derivative; combining the alkylated acetamide derivative and a concentrated hydrochloric acid in a methanol solvent at about 50° C. to remove the acetamide group and form a 2-amino-3,5-dihalo-4-alkylaminopridine. 
 
     
     
       13. The method of  claim 12 , wherein
 (i) the 2-aminopyridine of reaction (i) comprises Formula (12), wherein R 23 , R 3 , and R 4  are as defined in  claim 1  and R 24  is hydrogen; and the 2-amino-5-chloropyridine derivative comprises Formula (12), wherein R 23 , R 3 , and R 4  are the same as for the 2-aminopyridine and R 24  is chloro; or 
 (ii) the substituted 2-aminopyridine comprises Formula (12), wherein R 23  is fluoro, chloro, or bromo; R 3  is hydrogen; R 4  is as defined in  claim 1 ; and R 24  is fluoro, chloro, or bromo; 
 
       
         
           
           
               
               
           
         
       
     
     
       14. The method of  claim 12 , wherein the amino pyridine compound is selected from the group consisting of:
 2-Amino-3-fluoro-4-methyl-5-chloropyridine; 
 2-Amino-3-ethyl-5-chloropyridine; 
 2-Amino-3-fluoro-4-ethyl-5-chloropyridine; and 
 2-Amino-4-methyl-3,5-difluoropyridine. 
 
     
     
       15. The compound of  claim 1 , wherein R 1  is a 2-Pyridyl ring of Formula (3) and at least one of R 3 , R 23 , or R 24  is fluoro or chloro. 
     
     
       16. The compound of  claim 1 , wherein R 1  is a 2-Pyridyl ring of Formula (3) and at least two of R 3 , R 23 , or R 24  is fluoro or chloro. 
     
     
       17. The compound of  claim 16 , wherein R 1  is a 2-Pyridyl ring of Formula (3) and at least one of R 23  or R 24  is fluoro or chloro. 
     
     
       18. The compound of  claim 16 , wherein R 24  is chloro. 
     
     
       19. The compound of  claim 1 , wherein R 1  is a 2-Pyridyl ring of Formula (3) and one of R 3 , R 4 , R 23 , or R 24  is methyl or ethyl and at least one of R 3 , R 4 , R 23 , or R 24  is halogen. 
     
     
       20. The compound of  claim 19 , R 24  is chloro and R 3 , R 4 , or R 23  is methyl or ethyl. 
     
     
       21. The compound of  claim 1 , wherein R 1  is a 2-Pyridyl ring of Formula (3) and none of R 3 , R 4 , R 23 , or R 24  is methyl. 
     
     
       22. The compound of  claim 1 , wherein R 1  is a 3-Pyridyl ring of Formula (4), each of R 5 , R 6 , and R 7  are hydrogen, and R 2  is a 2,4-dimethyl substituted phenyl ring. 
     
     
       23. The compound of  claim 1 , wherein R 1  is a 3-Pyridyl ring of Formula (4) and at least one of R 5 , R 6 , or R 7  is not hydrogen. 
     
     
       24. The compound of  claim 1 , wherein R 2  is
 a 2-chloro substituted phenyl ring; 
 a 2,3-dichloro substituted phenyl ring; 
 a 2,4-dichloro substituted phenyl ring; 
 a 2,5-dichloro substituted phenyl ring; 
 a 3,4-dichloro substituted phenyl ring; 
 a 2-chlor, 4-fluoro substituted phenyl ring; 
 a 4-trifluoromethyl substituted phenyl ring; 
 a 2-fluoro, 4-trifluoromethyl substituted phenyl ring; 
 a 2,4-dimethyl substituted phenyl ring; or 
 a 2,3,4-trimethoxy substituted phenyl ring. 
 
     
     
       25. The compound of  claim 1 , wherein X is hydrogen. 
     
     
       26. The compound of  claim 1 , selected from the group consisting of: